On Sep 28, 2004, at 7:24 PM, John Timmer wrote:
>>> Looks good, although I agree with Alex to put such functionality in
>> wrappers. Just a small comment, would you mind renaming it to
>> something
>> that starts with BCUtil... ?
>> No, no problem - I'll try to get to that tomorrow.
>> Just to comment on where Ranges are useful - let's say you want to
> mark a
> DNA sequence's ORFs >25bp long. You translate it, then ask the
> BCCodonSequence where the ORFs are. You create an ORF object, but then
> you're already two objects removed from the original sequence. The
> intermediate item, the CodonSequence, doesn't know about either of
> them, or
> how to keep all the information in synch if anything changes.
>> Returning an array of ranges will allow you to quickly mark them in the
> original sequence. I'm not saying there's no call for wrappers, just
> when
> there are obvious uses for something like a Range, you should also
> supply
> those methods.
What would be really nice for the user, is a wrapper that uses that
code (BCValueAdditions) to do everything behind the scenes. So you pass
a sequence, set some parameters, and get in return your array of
subsequences.
- Koen.